List of works - Stefan Klumpp

A model for sigma factor competition in bacterial cells

scientific article

A superresolution census of RNA polymerase

scientific article published on December 2013

ACTIVE BIO-SYSTEMS: FROM SINGLE MOTOR MOLECULES TO COOPERATIVE CARGO TRANSPORT

Active diffusion of motor particles.

scientific article

Asymmetric exclusion process with a dynamic roadblock and open boundaries

Asymmetric simple exclusion processes with diffusive bottlenecks

scientific article published on 02 December 2004

Backtracking dynamics of RNA polymerase: pausing and error correction

scientific article published on 15 August 2013

Bacterial growth: global effects on gene expression, growth feedback and proteome partition

scientific article published on 02 February 2014

Bacterial twitching motility is coordinated by a two-dimensional tug-of-war with directional memory

scientific article published on 7 May 2014

Bidirectional transport by molecular motors: enhanced processivity and response to external forces

scientific article

Biochemical reactions in crowded environments: revisiting the effects of volume exclusion with simulations

Biologically controlled synthesis and assembly of magnetite nanoparticles

scientific article

COOPERATIVE TRANSPORT BY SMALL TEAMS OF MOLECULAR MOTORS

Cargo Transport by Teams of Molecular Motors: Basic Mechanisms for Intracellular Drug Delivery

Chemotaxis in external fields: Simulations for active magnetic biological matter

scientific article published on 19 December 2019

Co-operative transport by molecular motors

scientific article published on October 2011

Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae

scientific article published on 4 September 2014

Cooperative behavior of molecular motors: Cargo transport and traffic phenomena

Cooperative cargo transport by several molecular motors

scientific article

Decoding Biomineralization: Interaction of a Mad10-Derived Peptide with Magnetite Thin Films

scientific article published on 07 October 2019

Deterministic and Stochastic Descriptions of Gene Expression Dynamics

article

Differences between cotranscriptional and free riboswitch folding

scientific article

Dilution and the theoretical description of growth-rate dependent gene expression

scientific article published on 16 September 2013

Distinct Transport Regimes of Two Elastically Coupled Molecular Motors

Distinct transport regimes for two elastically coupled molecular motors ⬇️

scientific article published on May 14, 2012

Diversity of magneto-aerotactic behaviors and oxygen sensing mechanisms in cultured magnetotactic bacteria

scientific article published on July 2014

Dynamic blockage in an exclusion process

Effects of the chemomechanical stepping cycle on the traffic of molecular motors

scientific article

Elastic Coupling Effects in Cooperative Transport by a Pair of Molecular Motors

Elastic Properties of Magnetosome Chains

Elastic properties of magnetosome chains

Emergence of phenotype switching through continuous and discontinuous evolutionary transitions.

scientific article

Emergence of robust growth laws from optimal regulation of ribosome synthesis

scientific article

Entrainment and Unit Velocity: Surprises in an Accelerated Exclusion Process

scientific article published on 27 September 2012

External forces influence the elastic coupling effects during cargo transport by molecular motors

scientific article published on 02 February 2015

Facilitated diffusion in the presence of obstacles on the DNA.

scientific article published in April 2016

Fast Magnetic Micropropellers with Random Shapes

scientific article

Growth rate-dependent global effects on gene expression in bacteria

scientific article published on December 2009

Growth-rate dependence reveals design principles of plasmid copy number control

scientific article

High-speed motility originates from cooperatively pushing and pulling flagella bundles in bilophotrichous bacteria

scientific article published on 28 January 2020

Impact of the cell division cycle on gene circuits

article

Influence of magnetic fields on magneto-aerotaxis

scientific article (publication date: 2014)

Interplay between population dynamics and drug tolerance of Staphylococcus aureus persister cells

scientific article published in January 2012

Interplay of Magnetic Interactions and Active Movements in the Formation of Magnetosome Chains ⬇️

scientific article published on March 19, 2012

Interplay of surface interaction and magnetic torque in single-cell motion of magnetotactic bacteria in microfluidic confinement

scientific article published in 2022

Is F1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip

scientific article published on 29 April 2019

Kinesin's backsteps under mechanical load

scientific article published on 18 May 2009

Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models

scientific article published on 4 November 2013

Life in crowded conditions

article

Magnetotactic bacteria

Mass transport perspective on an accelerated exclusion process: Analysis of augmented current and unit-velocity phases

scientific article published on 28 February 2013

Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments.

scientific article published on 10 October 2016

Mechanisms and economy of molecular machines

Modeling stochastic gene expression in growing cells

scientific article published on 28 January 2014

Molecular Motors: Cooperative Phenomena of Multiple Molecular Motors

Molecular crowding limits translation and cell growth

scientific article published on 30 September 2013

Molecular motor traffic in a half-open tube

Molecular motor traffic: From biological nanomachines to macroscopic transport

Motility States of Molecular Motors Engaged in a Stochastic Tug-of-War

Movements of molecular motors: Ratchets, random walks and traffic phenomena

Navigation with magnetic nanoparticles: magnetotactic bacteria and magnetic micro-robots

Noise-induced transport of two coupled particles

scientific article published on 27 February 2001

On Protein Folding in Crowded Conditions

scientific article published on 27 November 2019

On ribosome load, codon bias and protein abundance.

scientific article

Pausing and Backtracking in Transcription Under Dense Traffic Conditions

Phase transitions in systems with two species of molecular motors

Phenotypically heterogeneous populations in spatially heterogeneous environments.

scientific article published on 12 March 2014

Population dynamics of bacterial persistence

scientific article

Positioning the flagellum at the center of a dividing cell to combine bacterial division with magnetic polarity

scientific article

Probing the mechanical properties of magnetosome chains in living magnetotactic bacteria

scientific article published on 11 July 2014

Quantifying gliding forces of filamentous cyanobacteria by self-buckling

Random walks of cytoskeletal motors in open and closed compartments

scientific article

Random walks of molecular motors arising from diffusional encounters with immobilized filaments

scientific article published on 9 June 2004

Segregation of prokaryotic magnetosomes organelles is driven by treadmilling of a dynamic actin-like MamK filament

scientific article

Selecting for function: solution synthesis of magnetic nanopropellers

scientific article published on 22 October 2013

Self-organized density patterns of molecular motors in arrays of cytoskeletal filaments

scientific article published on May 2005

Simulation of colony pattern formation under differential adhesion and cell proliferation

scientific article published on 22 February 2018

Simulations of structure formation by confined dipolar active particles

scientific article published on 20 October 2020

Sources of stochasticity in constitutive and autoregulated gene expression

article

Steering magnetic micropropellers along independent trajectories

article published in 2015

Stochastic simulations of cargo transport by processive molecular motors

scientific article published in December 2009

Swimming with magnets: From biological organisms to synthetic devices

Traffic by Small Teams of Molecular Motors

Traffic by multiple species of molecular motors.

scientific article

Traffic of Molecular Motors

Traffic patrol in the transcription of ribosomal RNA.

scientific article published on 07 September 2009

Transcriptional proofreading in dense RNA polymerase traffic

Transport by Molecular Motors in the Presence of Static Defects

Transport of beads by several kinesin motors

scientific article

Tug-of-war as a cooperative mechanism for bidirectional cargo transport by molecular motors

scholarly article

List of works by Stefan Klumpp

A model for sigma factor competition in bacterial cells

A superresolution census of RNA polymerase

ACTIVE BIO-SYSTEMS: FROM SINGLE MOTOR MOLECULES TO COOPERATIVE CARGO TRANSPORT

Active diffusion of motor particles.

Asymmetric exclusion process with a dynamic roadblock and open boundaries

Asymmetric simple exclusion processes with diffusive bottlenecks

Backtracking dynamics of RNA polymerase: pausing and error correction

Bacterial growth: global effects on gene expression, growth feedback and proteome partition

Bacterial twitching motility is coordinated by a two-dimensional tug-of-war with directional memory

Bidirectional transport by molecular motors: enhanced processivity and response to external forces

Biochemical reactions in crowded environments: revisiting the effects of volume exclusion with simulations

Biologically controlled synthesis and assembly of magnetite nanoparticles

COOPERATIVE TRANSPORT BY SMALL TEAMS OF MOLECULAR MOTORS

Cargo Transport by Teams of Molecular Motors: Basic Mechanisms for Intracellular Drug Delivery

Chemotaxis in external fields: Simulations for active magnetic biological matter

Co-operative transport by molecular motors

Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae

Cooperative behavior of molecular motors: Cargo transport and traffic phenomena

Cooperative cargo transport by several molecular motors

Decoding Biomineralization: Interaction of a Mad10-Derived Peptide with Magnetite Thin Films

Deterministic and Stochastic Descriptions of Gene Expression Dynamics

Differences between cotranscriptional and free riboswitch folding

Dilution and the theoretical description of growth-rate dependent gene expression

Distinct Transport Regimes of Two Elastically Coupled Molecular Motors

Distinct transport regimes for two elastically coupled molecular motors ⬇️

Diversity of magneto-aerotactic behaviors and oxygen sensing mechanisms in cultured magnetotactic bacteria

Dynamic blockage in an exclusion process

Effects of the chemomechanical stepping cycle on the traffic of molecular motors

Elastic Coupling Effects in Cooperative Transport by a Pair of Molecular Motors

Elastic Properties of Magnetosome Chains

Elastic properties of magnetosome chains

Emergence of phenotype switching through continuous and discontinuous evolutionary transitions.

Emergence of robust growth laws from optimal regulation of ribosome synthesis

Entrainment and Unit Velocity: Surprises in an Accelerated Exclusion Process

External forces influence the elastic coupling effects during cargo transport by molecular motors

Facilitated diffusion in the presence of obstacles on the DNA.

Fast Magnetic Micropropellers with Random Shapes

Growth rate-dependent global effects on gene expression in bacteria

Growth-rate dependence reveals design principles of plasmid copy number control

High-speed motility originates from cooperatively pushing and pulling flagella bundles in bilophotrichous bacteria

Impact of the cell division cycle on gene circuits

Influence of magnetic fields on magneto-aerotaxis

Interplay between population dynamics and drug tolerance of Staphylococcus aureus persister cells

Interplay of Magnetic Interactions and Active Movements in the Formation of Magnetosome Chains ⬇️

Interplay of surface interaction and magnetic torque in single-cell motion of magnetotactic bacteria in microfluidic confinement

Is F1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip

Kinesin's backsteps under mechanical load

Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models

Life in crowded conditions

Magnetotactic bacteria

Mass transport perspective on an accelerated exclusion process: Analysis of augmented current and unit-velocity phases

Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments.

Mechanisms and economy of molecular machines

Modeling stochastic gene expression in growing cells

Molecular Motors: Cooperative Phenomena of Multiple Molecular Motors

Molecular crowding limits translation and cell growth

Molecular motor traffic in a half-open tube

Molecular motor traffic: From biological nanomachines to macroscopic transport

Motility States of Molecular Motors Engaged in a Stochastic Tug-of-War

Movements of molecular motors: Ratchets, random walks and traffic phenomena

Navigation with magnetic nanoparticles: magnetotactic bacteria and magnetic micro-robots

Noise-induced transport of two coupled particles

On Protein Folding in Crowded Conditions

On ribosome load, codon bias and protein abundance.

Pausing and Backtracking in Transcription Under Dense Traffic Conditions

Phase transitions in systems with two species of molecular motors

Phenotypically heterogeneous populations in spatially heterogeneous environments.

Population dynamics of bacterial persistence

Positioning the flagellum at the center of a dividing cell to combine bacterial division with magnetic polarity

Probing the mechanical properties of magnetosome chains in living magnetotactic bacteria

Quantifying gliding forces of filamentous cyanobacteria by self-buckling

Random walks of cytoskeletal motors in open and closed compartments

Random walks of molecular motors arising from diffusional encounters with immobilized filaments

Segregation of prokaryotic magnetosomes organelles is driven by treadmilling of a dynamic actin-like MamK filament

Selecting for function: solution synthesis of magnetic nanopropellers

Self-organized density patterns of molecular motors in arrays of cytoskeletal filaments

Simulation of colony pattern formation under differential adhesion and cell proliferation

Simulations of structure formation by confined dipolar active particles

Sources of stochasticity in constitutive and autoregulated gene expression